- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] e212f2: TabularData.set_peek() was missing parameters pres...
by GitHub 08 Sep '15

08 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e212f224703d4f63721eb51aa7214640c9e86c53 https://github.com/galaxyproject/galaxy/commit/e212f224703d4f63721eb51aa721… Author: Richard Burhans <burhans(a)bx.psu.edu> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- TabularData.set_peek() was missing parameters present in Text.set_peek() Changed default value of skipchars in Text.set_peek() from [] to None Commit: 65f6d83459cd82c22b7308d7fdb9ba35b973aca7 https://github.com/galaxyproject/galaxy/commit/65f6d83459cd82c22b7308d7fdb9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #705 from richard-burhans/tabulardata Fix to get custom datatypes working after TabularData class was added Compare: https://github.com/galaxyproject/galaxy/compare/26c79e4aab5b...65f6d83459cd

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[galaxyproject/usegalaxy-playbook] bbbdad: Mutable configs on Test
by GitHub 08 Sep '15

08 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bbbdadec9ee8e3f7cddf4ca2e41a17a848afdc20 https://github.com/galaxyproject/usegalaxy-playbook/commit/bbbdadec9ee8e3f7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml Log Message: ----------- Mutable configs on Test Commit: fb731fd2a8452a4401c1ffda40fca5e2cc33cfc2 https://github.com/galaxyproject/usegalaxy-playbook/commit/fb731fd2a8452a44… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/common/dynamic_rules/reserved.py Log Message: ----------- Add reserved partition users Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/d1ea56bcd75e...…

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[galaxyproject/galaxy] 9850e4: Fix regression introduced in 6c82266546c77361f9d22...
by GitHub 08 Sep '15

08 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9850e45f07ebca6109084cfe3bd1338b47b361ae https://github.com/galaxyproject/galaxy/commit/9850e45f07ebca6109084cfe3bd1… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Fix regression introduced in 6c82266546c77361f9d2265ab749db1446142150 . Fix traceback when calling galaxy.webapps.galaxy.controllers.admin_toolshed.AdminToolshed.update_to_changeset_revision() due to repository being None. Commit: 26c79e4aab5b8f9f0f7d0c5908352c776f12cef0 https://github.com/galaxyproject/galaxy/commit/26c79e4aab5b8f9f0f7d0c590835… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #701 from nsoranzo/fix_for_6c82266546c77361f9d2265ab749db1446142150 Fix regression introduced in 6c82266546c77361f9d2265ab749db1446142150 . Compare: https://github.com/galaxyproject/galaxy/compare/cafe2ece1e0a...26c79e4aab5b

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[galaxyproject/galaxy] 16a98b: Fixes to LDAP auth config sample.
by GitHub 04 Sep '15

04 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 16a98b50cce48150272289b409ae5a2a70fb9425 https://github.com/galaxyproject/galaxy/commit/16a98b50cce48150272289b409ae… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M config/auth_conf.xml.sample Log Message: ----------- Fixes to LDAP auth config sample. Commit: b962a8ded0661b1df940400cb544a0ddbcfb0686 https://github.com/galaxyproject/galaxy/commit/b962a8ded0661b1df940400cb544… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/galaxy/auth/__init__.py Log Message: ----------- Style fixes. Commit: 474d58809ab1a001a64cb2f540e896d2de22cda5 https://github.com/galaxyproject/galaxy/commit/474d58809ab1a001a64cb2f540e8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/mobile.py Log Message: ----------- Fix commented-out code. Commit: cafe2ece1e0a71870be6c368e569ff2b4ceab096 https://github.com/galaxyproject/galaxy/commit/cafe2ece1e0a71870be6c368e569… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M config/auth_conf.xml.sample M lib/galaxy/auth/__init__.py M lib/galaxy/webapps/galaxy/controllers/mobile.py Log Message: ----------- Merge pull request #696 from nsoranzo/dev Small fixes for LDAP auth. Compare: https://github.com/galaxyproject/galaxy/compare/2867f1149a01...cafe2ece1e0a

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[galaxyproject/galaxy] 197c7b: Fix for fix for fix for handling of unix permissio...
by GitHub 04 Sep '15

04 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 197c7b21b209a7b6fbdb9a8a11c232a2b88523fc https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix for fix for fix for handling of unix permissions in .zip files. Append common_prefix to extraction_path only when returning. Commit: 1203ccc49cbf8726bdf35441593eec0cf00df652 https://github.com/galaxyproject/galaxy/commit/1203ccc49cbf8726bdf35441593e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #689 from nsoranzo/release_15.07 [15.07] Fix for fix for fix for handling of unix permissions in .zip files. Commit: 2284b2242c72183b8218717ea728bdc0d2420ac8 https://github.com/galaxyproject/galaxy/commit/2284b2242c72183b8218717ea728… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'release_15.07' Commit: 2867f1149a019f840bc6f4d1da23b98aad702839 https://github.com/galaxyproject/galaxy/commit/2867f1149a019f840bc6f4d1da23… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/99e7ba43a0c4...2867f1149a01

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[galaxyproject/galaxy] 197c7b: Fix for fix for fix for handling of unix permissio...
by GitHub 04 Sep '15

04 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 197c7b21b209a7b6fbdb9a8a11c232a2b88523fc https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix for fix for fix for handling of unix permissions in .zip files. Append common_prefix to extraction_path only when returning. Commit: 1203ccc49cbf8726bdf35441593eec0cf00df652 https://github.com/galaxyproject/galaxy/commit/1203ccc49cbf8726bdf35441593e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #689 from nsoranzo/release_15.07 [15.07] Fix for fix for fix for handling of unix permissions in .zip files. Commit: 2284b2242c72183b8218717ea728bdc0d2420ac8 https://github.com/galaxyproject/galaxy/commit/2284b2242c72183b8218717ea728… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge branch 'release_15.07' Compare: https://github.com/galaxyproject/galaxy/compare/4557b27fea51...2284b2242c72

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[galaxyproject/galaxy] 197c7b: Fix for fix for fix for handling of unix permissio...
by GitHub 04 Sep '15

04 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 197c7b21b209a7b6fbdb9a8a11c232a2b88523fc https://github.com/galaxyproject/galaxy/commit/197c7b21b209a7b6fbdb9a8a11c2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Fix for fix for fix for handling of unix permissions in .zip files. Append common_prefix to extraction_path only when returning. Commit: 1203ccc49cbf8726bdf35441593eec0cf00df652 https://github.com/galaxyproject/galaxy/commit/1203ccc49cbf8726bdf35441593e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #689 from nsoranzo/release_15.07 [15.07] Fix for fix for fix for handling of unix permissions in .zip files. Compare: https://github.com/galaxyproject/galaxy/compare/990501d2d947...1203ccc49cbf

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[galaxyproject/galaxy] 8430ca: UI, histories: correct allFetched setting in setCo...
by GitHub 03 Sep '15

03 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8430ca4e3fc506db41357312db0cced248ee43dd https://github.com/galaxyproject/galaxy/commit/8430ca4e3fc506db41357312db0c… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- UI, histories: correct allFetched setting in setCollection to allow fetching after changing collection order Commit: b325966e65398b6f7ff6bf493c44e2ab691cd042 https://github.com/galaxyproject/galaxy/commit/b325966e65398b6f7ff6bf493c44… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/style/less/history.less M static/style/blue/base.css Log Message: ----------- UI, histories: try to correct bootstrap popover dropdown width to keep caret inside button Commit: 99e7ba43a0c45a8777aafb0c5d0d9e773793d201 https://github.com/galaxyproject/galaxy/commit/99e7ba43a0c45a8777aafb0c5d0d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/style/less/history.less M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/multi-panel.js M static/style/blue/base.css Log Message: ----------- Merge pull request #695 from carlfeberhard/multi-history.all-fetched Fix multi-history fetch flag to allow re-fetching after collection sort Compare: https://github.com/galaxyproject/galaxy/compare/9df1dfafebe3...99e7ba43a0c4

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[galaxyproject/galaxy] 85d4b7: Slight refactoring of parse_int, move to galaxy.ut...
by GitHub 03 Sep '15

03 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85d4b747297f8bb2a2d7e39c8995d92e6e91911b https://github.com/galaxyproject/galaxy/commit/85d4b747297f8bb2a2d7e39c8995… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Slight refactoring of parse_int, move to galaxy.util and use default in invocation. Commit: 67322c5a440e2912be02c88d4d77e525fe8a7638 https://github.com/galaxyproject/galaxy/commit/67322c5a440e2912be02c88d4d77… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-01 (Tue, 01 Sep 2015) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Don't overload language builtins min, max in parse_int Commit: 65182d3a623630a783aff3a1d4ebba14bb106e81 https://github.com/galaxyproject/galaxy/commit/65182d3a623630a783aff3a1d4eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-02 (Wed, 02 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Include second file of commit fixing min/max overloading Commit: 2afcc658c7f4b7f945413050b5b7bdcdd0b3abaf https://github.com/galaxyproject/galaxy/commit/2afcc658c7f4b7f945413050b5b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Support 'None' and raise the ValueError when appropriate. Commit: 9df1dfafebe31c84d546aee4146be1239cc793dc https://github.com/galaxyproject/galaxy/commit/9df1dfafebe31c84d546aee4146b… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #684 from dannon/minor_parseint_tweaks Minor parseint refactoring, tweaks Compare: https://github.com/galaxyproject/galaxy/compare/39c2854f6525...9df1dfafebe3

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[galaxyproject/galaxy] 152c81: Set a default value for copy history dialog radio ...
by GitHub 03 Sep '15

03 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 152c81cf8acc45b1c686e26eba04ec87488c52a1 https://github.com/galaxyproject/galaxy/commit/152c81cf8acc45b1c686e26eba04… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M templates/webapps/galaxy/history/copy.mako Log Message: ----------- Set a default value for copy history dialog radio input (to copy *all*). Commit: 39c2854f652524f784a5179a7a2762fd375d67e5 https://github.com/galaxyproject/galaxy/commit/39c2854f652524f784a5179a7a27… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M templates/webapps/galaxy/history/copy.mako Log Message: ----------- Merge pull request #693 from dannon/copy_history_default Set a default value for copy history dialog radio input (to copy *all*). Compare: https://github.com/galaxyproject/galaxy/compare/0785dedd854c...39c2854f6525

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